A short history of the initial application of anti-5-BrdU to the detection and measurement of S phase

CDKL3 is a targetable regulator of cell cycle progression in cancers

Cell cycle regulation is largely abnormal in cancers. Molecular understanding and therapeutic targeting of the aberrant cell cycle are essential. Here, we identified that an underappreciated serine/threonine kinase, cyclin-dependent kinase-like 3 (CDKL3), crucially drives rapid cell cycle progression and cell growth in cancers. With regard to mechanism, CDKL3 localizes in the nucleus and associates with specific cyclin to directly phosphorylate retinoblastoma (Rb) for quiescence exit. In parallel, CDKL3 prevents the ubiquitin-proteasomal degradation of cyclin-dependent kinase 4 (CDK4) by direct phosphorylation on T172 to sustain G1 phase advancement. The crucial function of CDKL3 in cancers was demonstrated both in vitro and in vivo. We also designed, synthesized, and characterized a first-in-class CDKL3-specific inhibitor, HZ1. HZ1 exhibits greater potency than CDK4/6 inhibitor in pan-cancer treatment by causing cell cycle arrest and overcomes acquired resistance to CDK4/6 inhibitor. In particular, CDKL3 has significant clinical relevance in colon cancer, and the effectiveness of HZ1 was demonstrated by murine and patient-derived cancer models. Collectively, this work presents an integrated paradigm of cancer cell cycle regulation and suggests CDKL3 targeting as a feasible approach in cancer treatment.

Determining reference ranges for lymphocyte proliferation responses to phytohemagglutinin and Bacillus Calmette-Guérin in Iranian children

PURPOSE

To establish reference ranges (RRs) for stimulation index of T cell proliferation triggered by phytohemagglutinin (PHA-SI) and Bacillus Calmette-Guérin (BCG-SI).

METHODS

This study investigated data from 359 healthy children and 35 patients with cellular immunodeficiency as positive controls (2010-2021). We applied a colorimetric-based method (BrdU) to measure proliferation and determine the RRs at the 2.5th and 97.5th percentiles (95% confidence intervals). A cross-validation approach was performed.

RESULTS

In healthy controls, the RRs for PHA-SI and BCG-SI ranged between 3 and 5.2 and 2.52 to 5.2, respectively. PHA-SI and BCG-SI were in Severe Combined Immunodeficiency (SCID) patients from 1.2 to 2.5 and 0 to 2, while in Mendelian susceptibility to mycobacterial diseases (MSMD) patients, 2.53 to 4.5 and 0.74 to 2.2, respectively. The thresholds' accuracy was checked for testing reference intervals with diagnostic effects.

CONCLUSION

This study establishes PHA-SI and BCG-SI reference ranges to aid in diagnosing and treating congenital immunodeficiency diseases.

Cell viability and cytotoxicity assays: Biochemical elements and cellular compartments

Cell viability and cytotoxicity assays play a crucial role in drug screening and evaluating the cytotoxic effects of various chemicals. The quantification of cell viability and proliferation serves as the cornerstone for numerous in vitro assays that assess cellular responses to external factors. In the last decade, several studies have developed guidelines for defining and interpreting cell viability and cytotoxicity based on morphological, biochemical, and functional perspectives. As this domain continues to experience ongoing growth, revealing new mechanisms orchestrating diverse cell cytotoxicity pathways, we suggest a revised classification for multiple assays employed in evaluating cell viability and cell death. This classification is rooted in the cellular compartment and/or biochemical element involved, with a specific focus on mechanistic and essential aspects of the process. The assays are founded on diverse cell functions, encompassing metabolic activity, enzyme activity, cell membrane permeability and integrity, adenosine 5'-triphosphate content, cell adherence, reduction equivalents, dye inclusion or exclusion, constitutive protease activity, colony formation, DNA fragmentation and nuclear splitting. These assays present straightforward, reliable, sensitive, reproducible, cost-effective, and high-throughput approaches for appraising the effects of newly formulated chemotherapeutic biomolecules on the cell survival during the drug development process.

5-Bromo-2'-deoxyuridine labeling: historical perspectives, factors influencing the detection, toxicity, and its implications in the neurogenesis

The halopyrimidine 5-bromo-2'-deoxyuridine (BrdU) is an exogenous marker of DNA synthesis. Since the introduction of monoclonal antibodies against BrdU, an increasing number of methodologies have been used for the immunodetection of this synthesized bromine-tagged base analogue into replicating DNA. BrdU labeling is widely used for identifying neuron precursors and following their fate during the embryonic, perinatal, and adult neurogenesis in a variety of vertebrate species including birds, reptiles, and mammals. Due to BrdU toxicity, its incorporation into replicating DNA presents adverse consequences on the generation, survival, and settled patterns of cells. This may lead to false results and misinterpretation in the identification of proliferative neuroblasts. In this review, I will indicate the detrimental effects of this nucleoside during the development of the central nervous system, as well as the reliability of BrdU labeling to detect proliferating neuroblasts. Moreover, it will show factors influencing BrdU immunodetection and the contribution of this nucleoside to the study of prenatal, perinatal, and adult neurogenesis. Human adult neurogenesis will also be discussed. It is my hope that this review serves as a reference for those researchers who focused on detecting cells that are in the synthetic phase of the cell cycle.

Monitoring the Cell Cycle of Tumor Cells in Mouse Models of Human Cancer

Cell division is obligatory to tumor growth. However, both cancer cells and noncancer cells in tumors can be found in distinct stages of the cell cycle, which may inform the growth potential of these tumors, their propensity to metastasize, and their response to therapy. Hence, it is of utmost importance to monitor the cell cycle of tumor cells. Here we discuss well-established methods and new genetic advances to track the cell cycle of tumor cells in mouse models of human cancer. We also review recent genetic studies investigating the role of the cell-cycle machinery in the growth of tumors in vivo, with a focus on the machinery regulating the G1/S transition of the cell cycle.

The Effect of Circumscribed Exposure to the Pan-Aurora Kinase Inhibitor VX-680 on Proliferating Euploid Cells

Small molecule inhibitors of aurora kinases are currently being investigated in oncology clinical trials. The long-term effects of these inhibitors on proliferating euploid cells have not been adequately studied. We examined the effect of the reversible pan-aurora kinase inhibitor VX-680 on p53-competent human euploid cells. Circumscribed treatment with VX-680 blocked cytokinesis and arrested cells in G1 or a G1-like status. Approximately 70% of proliferatively arrested cells had 4N DNA content and abnormal nuclei. The remaining 30% of cells possessed 2N DNA content and normal nuclei. The proliferative arrest was not due to the activation of the tumor suppressor Rb and was instead associated with rapid induction of the p53–p21 pathway and p16. The induction was particularly evident in cells with nuclear abnormalities but was independent of activation of the DNA damage response. All of these effects were correlated with the potent inhibition of aurora kinase B. After release from VX-680, the cells with normal nuclei robustly resumed proliferation whereas the cells with abnormal nuclei underwent senescence. Irrespective of their nuclear morphology or DNA content, cells pre-treated with VX-680 failed to grow in soft agar or form tumors in mice. Our findings indicate that an intermittent treatment strategy might minimize the on-target side effects of Aurora Kinase B (AURKB) inhibitory therapies. The strategy allows a significant fraction of dividing normal cells to resume proliferation.

In Vivo Methods to Monitor Cardiomyocyte Proliferation

Adult mammalian cardiomyocytes demonstrate scarce cycling and even lower proliferation rates in response to injury. Signals that enhance cardiomyocyte proliferation after injury will be groundbreaking, address unmet clinical needs, and represent new strategies to treat cardiovascular diseases. In vivo methods to monitor cardiomyocyte proliferation are critical to addressing this challenge. Fortunately, advances in transgenic approaches provide sophisticated techniques to quantify cardiomyocyte cycling and proliferation.

Evaluation of the Response of HOS and Saos-2 Osteosarcoma Cell Lines When Exposed to Different Sizes and Concentrations of Silver Nanoparticles

Osteosarcoma is considered to be a highly malignant tumor affecting primarily long bones. It metastasizes widely, primarily to the lungs, resulting in poor survival rates of between 19 and 30%. Standard treatment consists of surgical removal of the affected site, with neoadjuvant and adjuvant chemotherapy commonly used, with the usual side effects and complications. There is a need for new treatments in this area, and silver nanoparticles (AgNPs) are one potential avenue for exploration. AgNPs have been found to possess antitumor and cytotoxic activity in vitro, by demonstrating decreased viability of cancer cells through cell cycle arrest and subsequent apoptosis. Integral to these pathways is tumor protein p53, a tumor suppressor which plays a critical role in maintaining genome stability by regulating cell division, after DNA damage. The purpose of this study was to determine if p53 mediates any difference in the response of the osteosarcoma cells in vitro when different sizes and concentrations of AgNPs are administered. Two cell lines were studied: p53-expressing HOS cells and p53-deficient Saos-2 cells. The results of this study suggest that the presence of protein p53 significantly affects the efficacy of AgNPs on osteosarcoma cells.

Maduramicin arrests myocardial cells at G0/G1 phase of the cell cycle through inhibiting AKT-Cyclin D1 signaling

Maduramicin, a polyether ionophore antibiotic used as an anticoccidial feed additive in poultry, is toxic to animals and humans and can cause heart failure. The present study was initiated to explore the underlying mechanism of toxicity in H9c2 myocardial cells. We observed using cell imaging and counting methods that maduramicin inhibited cell growth in a concentration-dependent manner. Furthermore, MTT assays showed that maduramicin inhibited cell proliferation in a concentration- and time-dependent manner, and was also confirmed by the finding that maduramicin time dependently blocked the incorporation of BrdU into DNA in H9c2 myocardial cells. Further studies revealed that maduramicin induced accumulation of the cells at G₀/G₁ phase of the cell cycle and concurrently, there was down regulation of expression of Cyclin D1. In addition, exposure to maduramicin pruned phosphorylation of AKT at both T308 and S473 sites. Finally, we found that pre-treatment of H9c2 myocardial cells with AKT activator SC79, attenuated the inhibitory effects of maduramicin on Cyclin D1 expression and cell proliferation. Collectively, our results suggest that maduramicin-suppressed AKT-Cyclin D1 signaling which results in G₀/G₁ phase cell cycle arrest, leading to the inhibition of myocardial cell proliferation.

Adult Hippocampal Neurogenesis in Major Depressive Disorder and Alzheimer's Disease

Depression and dementia are major public health problems. Major depressive disorder (MDD) and Alzheimer's disease (AD) reciprocally elevate the risk for one another. No effective drug is available to treat AD and about one-third of depressive patients show treatment resistance. The biological connection between MDD and AD is still unclear. Uncovering this link might open novel ways of treatment and prevention to improve patient healthcare. Here, we discuss recent studies specifically on the role of human adult hippocampal neurogenesis (AHN) in MDD and AD. We compare diverse approaches to analyse the effect of MDD and AD on human AHN and analyse different studies implicating the role of human AHN as a potential converging mechanism in MDD and AD.

SIRF: A Single-cell Assay for in situ Protein Interaction with Nascent DNA Replication Forks

The duplication of DNA is a fundamental process that is required for the transfer of the genetic information from parent to daughter cells. Aberrant DNA replication processes are associated with diverse disease phenotypes, including developmental defects, ageing disorders, blood disorders such as Fanconi Anemia, increased inflammation and cancer. Therefore, the development of tools to study proteins associated with error-free DNA replication processes is of paramount importance. So far, methods to study proteins associated with nascent replication forks relied on conventional immunofluorescence and immunoprecipitation assays of 5'-ethylene-2'-deoxyuridine (EdU) labeled DNA (iPOND). While greatly informative and important, these methods lack specificities for nascent fork interactions (e.g., IF) or assay an average change of millions of cells without single-cell resolution (e.g., iPOND). The assay system described here combines proximity ligation assay (PLA) with EdU coupled click-iT chemistry, which we termed "in situ protein interaction with nascent DNA replication forks (SIRF)". This method enables sensitive and quantitative analysis of protein interactions with nascent DNA replication forks with single-cell resolution, and can further be paired with conventional immunofluorescence marker analysis for added multi-parameter analysis.

cCMP and cUMP in Apoptosis: Concepts and Methods

The cyclic nucleotides cAMP and cGMP are well-characterized second messenger molecules regulating many important intracellular processes, such as differentiation, proliferation, and apoptosis. The latter is a highly regulated process of programmed cell death wherein several regulatory proteins, like those belonging to the Bcl-2 family, are involved. The initiation of apoptosis is regulated by three different pathways: the intrinsic or mitochondrial, the extrinsic, and the ER stress pathway. Recently, it has been published that the pyrimidine cyclic nucleotides cCMP and cUMP also function as second messenger molecules, and additionally have an effect on apoptosis signaling pathways. cCMP induced PKA-independent apoptosis via the intrinsic and ER-stress pathway in S49 mouse lymphoma cells, and cCMP as well as cUMP induced apoptosis in human HEL cells via the intrinsic pathway. However, in human K-562 cells, which are known to be multidrug-resistant, cCMP and cUMP had no effect. Summarized in this chapter are the initiation of apoptosis by cCMP and cUMP regarding the various apoptotic pathways, the enzymes involved in apoptosis, as well as the most relevant methods for the detection and examination of apoptosis and the corresponding signaling pathways.

Click Chemistry for Analysis of Cell Proliferation in Flow Cytometry

The measurement of cellular proliferation is fundamental to the assessment of cellular health, genotoxicity, and the evaluation of drug efficacy. Labeling, detection, and quantification of cells in the synthesis phase of cell cycle progression are not only important for characterizing basic biology, but also in defining cellular responses to drug treatments. Changes in DNA replication during S-phase can provide valuable insights into mechanisms of cell growth, cell cycle kinetics, and cytotoxicity. A common method for detection of cell proliferation is the incorporation of a thymidine analog during DNA synthesis. This chapter presents a pulse labeling method using the thymidine analog, 5-ethynyl-2'-deoxyuridine (EdU), with subsequent detection by click chemistry. EdU detection using click chemistry is bio-orthogonal to most living systems and does not non-specifically label other biomolecules. Live cells are first pulsed with EdU. After antibody labeling cell surface markers, fixation, and permeabilization, the incorporated EdU is covalently labeled using click chemistry thereby identifying proliferating cells. Improvements in click chemistry allow for labeling in the presence of fluorescent proteins and phycobiliproteins without quenching due to copper. Measuring DNA replication during cell cycle progression has cell health applications in flow cytometry, fluorescence microscopy, and high content imaging. This protocol has been developed and optimized for research use only and is not suitable for use in diagnostic procedures. © 2017 by John Wiley & Sons, Inc.

CyTOF Mass Cytometry for Click Proliferation Assays

Novel cell analyzers, including polychromatic flow cytometers and isotopical cytometry by time of flight (CyTOF) mass cytometers, enable simultaneous measurement of virtually bondless characteristics at the single-cell level. BrdU assays for quantifying cellular proliferation are common but have several limitations, including the need for a DNA denaturation step and inability to simultaneously resolve multiple parameters and phenotypic complexity. Click chemistry reactions have become popular in the past decade, as they can resolve these issues. This protocol introduces a novel assay able to bridge flow cytometry and CyTOF analysis for active S-phase determination in cell cycle applications, combining well-established click chemistry with a novel iodo-deoxyuridine (IdU) azide derivative and a cross-reactive anti-IdU antibody for detecting incorporated EdU during DNA synthesis. This method is preferred over traditional BrdU-based assays for complex and multiparametric experiments. It provides a feasible cost-effective approach for detecting ethynyl-labeled nucleotides, with the advantage of combining flow and mass cytometry analyses. © 2017 by John Wiley & Sons, Inc.

Long-term effects of autoimmune CNS inflammation on adult hippocampal neurogenesis

Neurogenesis is a well-characterized phenomenon within the dentate gyrus (DG) of the adult hippocampus. Aging and chronic degenerative disorders have been shown to impair hippocampal neurogenesis, but the consequence of chronic inflammation remains controversial. In this study the chronic experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis was used to investigate the long-term effects of T cell-mediated central nervous system inflammation on hippocampal neurogenesis. 5-Bromodeoxyuridine (BrdU)-labeled subpopulations of hippocampal cells in EAE and control mice (coexpressing GFAP, doublecortin, NeuN, calretinin, and S100) were quantified at the recovery phase, 21 days after BrdU administration, to estimate alterations on the rate and differentiation pattern of the neurogenesis process. The core features of EAE mice DG are (i) elevated number of newborn (BrdU+) cells indicating vigorous proliferation, which in the long term subsided; (ii) enhanced migration of newborn cells into the granule cell layer; (iii) increased level of immature neuronal markers (including calretinin and doublecortin); (iv) trending decrease in the percentage of newborn mature neurons; and (v) augmented gliogenesis and differentiation of newborn neural precursor cells (NPCs) to mature astrocytes (BrdU+/S100+). Although the inflammatory environment in the brain of EAE mice enhances the proliferation of hippocampal NPCs, in the long term neurogenesis is progressively depleted, giving prominence to gliogenesis. The discrepancy between the high number of immature cells and the low number of mature newborn cells could be the result of a caused defect in the maturation pathway. © 2016 Wiley Periodicals, Inc.

Experimental Approaches to Study Mitochondrial Localization and Function of a Nuclear Cell Cycle Kinase, Cdk1

Although mitochondria possess their own transcriptional machinery, merely 1% of mitochondrial proteins are synthesized inside the organelle. The nuclear-encoded proteins are transported into mitochondria guided by their mitochondria targeting sequences (MTS); however, a majority of mitochondrial localized proteins lack an identifiable MTS. Nevertheless, the fact that MTS can instruct proteins to go into the mitochondria provides a valuable tool for studying mitochondrial functions of normally nuclear and/or cytoplasmic proteins. We have recently identified the cell cycle kinase CyclinB1/Cdk1 complex in the mitochondria. To specifically study the mitochondrial functions of this complex, mitochondrial overexpression and knock-down of this complex without interfering with its nuclear or cytoplasmic functions were essential. By tagging CyclinB1/Cdk1 with MTS, we were able to achieve mitochondrial overexpression of this complex to study its mitochondrial targets as well as functions. Via tagging dominant-negative Cdk1 with MTS, inhibition of Cdk1 activity was accomplished particularly in the mitochondria. Potential mitochondrial targets of CyclinB1/Cdk1 complex were identified using a gel-based proteomics approach. Unlike traditional 2D gel analysis, we employed 2-dimensional difference gel electrophoresis (2D-DIGE) technology followed by phosphoprotein staining to fluorescently label differentially phosphorylated proteins in mitochondrial Cdk1 expressing cells. Identification of phosphoprotein spots that were altered in wild type versus dominant negative Cdk1 bearing mitochondria revealed the identity of mitochondrial targets of Cdk1. Finally, to determine the effect of CyclinB1/Cdk1 mitochondrial localization in cell cycle progression, a cell proliferation assay using a synthetic thymidine analogue EdU (5-ethynyl-2'-deoxyuridine) was used to monitor the cells as they go through the cell cycle and replicate their DNA. Altogether, we demonstrated a variety of approaches available to study mitochondrial localization and activity of a cell cycle kinase. These are advanced, yet easy to follow methods that will be beneficial to many cell biology researchers.

Anti-proliferative actions of a synthetic REV-ERBα/β agonist in breast cancer cells

REV-ERBα and REV-ERBβ are nuclear receptors that are ligand-dependent transcriptional repressors. Heme is the natural ligand for these receptors, but several synthetic agonists and antagonists have been designed recently. The gene that encodes REV-ERBα, NR1D1, is closely associated with ERBB2, the gene that encodes the HER2 oncogene, which is amplified in HER2(+) breast cancers. We examined the effect of a synthetic REV-ERB agonist, SR9011, on a range of estrogen receptor positive (ER(+)), ER(-), HER2(+), HER2(-) and triple negative breast cancer cell lines. We found that SR9011 suppressed proliferation of the breast cancer cell lines regardless of their ER or HER2 status. SR9011 had no effect on MCF10A cell proliferation. SR9011 appears to pause the cell cycle of the breast cancer cells prior to M phase. Cyclin A (CCNA2) was identified as a direct target gene of REV-ERB suggesting that suppression of expression of this cyclin by SR9011 may mediate the cell cycle arrest. These data indicate that synthetic REV-ERB ligands may hold utility in treatment of diseases associated with uncontrolled cellular proliferation such as cancer.

Scientific and Regulatory Policy Committee (SRPC) Review*

Increased cell proliferation is a central key event in the mode of action for many non-genotoxic carcinogens, and quantitative cell proliferation data play an important role in the cancer risk assessment of many pharmaceutical and environmental compounds. Currently, there is limited unified information on assay standards, reference values, targeted applications, study design issues, and quality control considerations for proliferation data. Here, we review issues in measuring cell proliferation indices, considerations for targeted studies, and applications within current risk assessment frameworks. As the regulatory environment moves toward more prospective evaluations based on quantitative pathway-based models, standardization of proliferation assays will become an increasingly important part of cancer risk assessment. To help address this development, we also discuss the potential role for proliferation data as a component of alternative carcinogenicity testing models. This information should improve consistency of cell proliferation methods and increase efficiency of targeted testing strategies.

A pulse-chase strategy combining click-EdU and photoconvertible fluorescent reporter: tracking Golgi protein dynamics during the cell cycle

Imaging or quantifying protein synthesis in cellulo through a well-resolved analysis of the cell cycle (also defining G1 subcompartments) is a methodological challenge. Click chemistry is the method of choice to reveal the thymidine analogue 5-ethynyl-2'-deoxyuridine (EdU) and track proliferating nuclei undergoing DNA synthesis. However, the click reaction quenches fluorescent proteins. Our challenge was to reconcile these two tools. A robust protocol based on a high-resolution cytometric cell cycle analysis in tobacco (Nicotiana tabacum) BY2 cells expressing fluorescent Golgi markers has been established. This was broadly applicable to tissues, cell clusters, and other eukaryotic material, and compatible with Scale clearing. EdU was then used with the photoconvertible protein sialyl transferase (ST)-Kaede as a Golgi marker in a photoconversion pulse-chase cytometric configuration resolving, in addition, subcompartments of G1. Quantitative restoration of protein fluorescence was achieved by introducing acidic EDTA washes to strip the copper from these proteins which were then imaged at neutral pH. The rate of synthesis of this Golgi membrane marker was low during early G1, but in the second half of G1 (30% of cycle duration) much of the synthesis occurred. Marker synthesis then persisted during S and G2. These insights into Golgi biology are discussed in terms of the cell's ability to adapt exocytosis to cell growth needs.

Pushing the frontiers of T-cell vaccines: accurate measurement of human T-cell responses

There is a need for novel approaches to tackle major vaccine challenges such as malaria, tuberculosis and HIV, among others. Success will require vaccines able to induce a cytotoxic T-cell response--a deficiency of most current vaccine approaches. The successful development of T-cell vaccines faces many hurdles, not least being the lack of consensus on a standardized T-cell assay format able to be used as a correlate of vaccine efficacy. Hence, there remains a need for reproducible measures of T-cell immunity proven in human clinical trials to correlate with vaccine protection. The T-cell equivalent of a neutralizing antibody assay would greatly accelerate the development and commercialization of T-cell vaccines. Recent advances have seen a plethora of new T-cell assays become available, including some like cytometry by time-of-flight with extreme multiparameter T-cell phenotyping capability. However, whether it is historic thymidine-based proliferation assays or sophisticated new cytometry assays, each assay has its relative advantages and disadvantages, and relatively few of these assays have yet to be validated in large-scale human vaccine trials. This review examines the current range of T-cell assays and assesses their suitability for use in human vaccine trials. Should one or more of these assays be accepted as an agreed surrogate of T-cell protection by a regulatory agency, this would significantly accelerate the development of T-cell vaccines.

Dual-pulse labeling using 5-ethynyl-2'-deoxyuridine (EdU) and 5-bromo-2'-deoxyuridine (BrdU) in flow cytometry

Changes in DNA replication during S-phase can give insights into mechanisms of cell growth, cell cycle kinetics, and cytotoxicity. A common method for detection of cell proliferation utilizes the incorporation of a thymidine analog during DNA synthesis. Incorporation of multiple analogs at different time points can further define cell cycle kinetics. Traditionally, the dual-pulse method has been done by combining 5-bromo-2'-deoxyuridine (BrdU) with iododeoxyuridine or chlorodeoxyuridine, with detection using multiple cross-reacting BrdU antibodies. This unit presents a dual-pulse method using the thymidine analog 5-ethyl-2'-deoxyuridine (EdU), detected by click chemistry, combined with BrdU labeling and detection. No cross reactivity with incorporated EdU is observed using the BrdU antibody clone MoBU-1. EdU detection using click chemistry does not cross-react with incorporated BrdU. Cells are first pulsed with EdU, and then pulsed with BrdU; sequential pulses of EdU, followed by BrdU, are done without removing or washing out EdU.

Cytometry of DNA replication and RNA synthesis: Historical perspective and recent advances based on "click chemistry"

This review covers progress in the development of cytometric methodologies designed to assess DNA replication and RNA synthesis. The early approaches utilizing autoradiography to detect incorporation of (3) H- or (14) C-labeled thymidine were able to identify the four fundamental phases of the cell cycle G(1) , S, G(2) , and M, and by analysis of the fraction of labeled mitosis (FLM), to precisely define the kinetics of cell progression through these phases. Analysis of (3) H-uridine incorporation and RNA content provided the means to distinguish quiescent G(0) from cycling G(1) cells. Subsequent progress in analysis of DNA replication was based on the use of BrdU as a DNA precursor and its detection by the quenching of the fluorescence intensity of DNA-bound fluorochromes such as Hoechst 33358 or acridine orange as measured by flow cytometry. Several variants of this methodology have been designed and used in studies to detect anticancer drug-induced perturbations of cell cycle kinetics. The next phase of method development, which was particularly useful in studies of the cell cycle in vivo, including clinical applications, relied on immunocytochemical detection of incorporated halogenated DNA or RNA precursors. This approach however was hampered by the need for DNA denaturation, which made it difficult to concurrently detect other cell constituents for multiparametric analysis. The recently introduced "click chemistry" approach has no such limitation and is the method of choice for analysis of DNA replication and RNA synthesis. This method is based on the use of 5-ethynyl-2'deoxyuridine (EdU) as a DNA precursor or 5-ethynyluridine (EU) as an RNA precursor and their detection with fluorochrome-tagged azides utilizing a copper (I) catalyzed [3+2] cycloaddition. Several examples are presented that illustrate incorporation of EdU or EU in cells subjected to DNA damage detected as histone H2AX phosphorylation that have been analyzed by flow or laser scanning cytometry.

Fluorogenic “click” reaction for labeling and detection of DNA in proliferating cells

A thymidine analog, 5-ethynyl-2′-deoxyuridine (EdU), has been reported as a rapid labeling tool for direct measurement of cells in S-phase. The alkynyl group of EdU is a biologically inert group that undergoes an extremely selective reaction with azido-functionalized groups via Cu(I)-catalyzed alkyneazide cycloaddition (CuAAC or “click”) reaction. Here we report the highly efficient reaction of the terminal alkynyl group of EdU with a pro-fluorogenic compound, 3-azido-7-hydroxycoumarin, to afford an intense fluorescent 1,2,3-triazole product, which occurs only after the CuAAC reaction. This new method eliminates concerns for residual fluorescence since the unreacted precursors are optically inactive. The procedure therefore does not require extensive wash steps to remove the unreacted fluorescent dyes in the sample, allowing for immediate quantification and visualization after the reaction. The advantage over currently available commercial products is its potential to streamline high-throughput applications and help minimize errors.

Cytometry and DNA ploidy: clinical uses and molecular perspective in gastric and lung cancer

Flow cytometry is one of the most powerful and specific methods used for the integrated study of the molecular and morphological events occurring during cell proliferation. Many methods have been described for investigating this process. Several cell cycle regulators controlling the correct entry and progression through the cell cycle are altered in tumors. In fact, in most, if not all, human cancers there is a deregulated control of G1 phase progression, the period when cells decide if they will start proliferation or stay quiescent. Cytometry (flow and image) is able to analyze DNA content thanks to the use of the same "molecule" conjugates with a fluorochrome that permits to identify DNA content of single cell in a sample. Most important results of studies on DNA ploidy have been reviewed during the last years and as a result the analyses of DNA ploidy in cancer may provide clinically useful information on diagnostic, therapeutic and prognostic aspects. In fact, aneuploid cancer has a high proliferative activity and a metastatic or invasive potential, markers of a poor prognosis. Multiparametric flow cytometry should allow the simultaneous determination of morphology, phenotype, intracellular protein expression, and status of chromatin and DNA. Evaluating if a particular protein is responsible for the aggressiveness of cancer, or the alteration of DNA content, or if the activation of its state is the cause of rapid growth of cancer cells, is very important and it can facilitate the clinical treatment of patients.

Exhaustive in vivo labelling of plasmid DNA with BrdU for intracellular detection in non-viral transfection of mammalian cells

The study of the non-viral gene delivery process at the molecular level, e.g. during the transfection of mammalian cells, is currently limited by the difficulties of specifically detecting the transfected plasmid DNA within the cells. Here we describe the in vivo production of 5-bromodeoxyuridine (BrdU)-labelled plasmid DNA by a thymine-requiring Escherichia coli strain leading to 92 +/- 15% BrdU incorporation while minimizing plasmid structure alteration. The labelled plasmid is produced on the milligram scale in a two-stage cultivation process. The relevance of this approach for plasmid DNA visualisation in the field of gene delivery is demonstrated by localising the BrdU-labelled plasmid DNA via immunodetection/fluorescence microscopy in CHO-K1 cells after electroporation with naked, BrdU-labelled plasmid DNA and after polyfection with polyethylenimine/BrdU-labelled plasmid complexes.

A survey of flow cytometry data analysis methods

Flow cytometry (FCM) is widely used in health research and in treatment for a variety of tasks, such as in the diagnosis and monitoring of leukemia and lymphoma patients, providing the counts of helper-T lymphocytes needed to monitor the course and treatment of HIV infection, the evaluation of peripheral blood hematopoietic stem cell grafts, and many other diseases. In practice, FCM data analysis is performed manually, a process that requires an inordinate amount of time and is error-prone, nonreproducible, nonstandardized, and not open for re-evaluation, making it the most limiting aspect of this technology. This paper reviews state-of-the-art FCM data analysis approaches using a framework introduced to report each of the components in a data analysis pipeline. Current challenges and possible future directions in developing fully automated FCM data analysis tools are also outlined.

Reaching for the other side: generating sequence-dependent interstrand cross-links with 5-bromodeoxyuridine and gamma-rays

Interstrand cross-links impede critical cellular processes such as transcription and replication and are thus considered to be one of the most toxic types of DNA damage. Although several studies now point to the existence of gamma-radiation-induced cross-links in cellular DNA, little is known about the characteristics required for their creation. Recently, we reported the formation of interstrand cross-links that were specific for mismatched nucleotides within 5-bromo-2'-deoxyuridine-substituted DNA. Given the structural specificity for interstrand cross-link formation, it is likely that open or mismatched regions of DNA in cells may be particularly favorable for cross-link production. Herein, we investigated the effect of the local DNA sequence on the formation of interstrand cross-links, using 5-bromo-2'-deoxyuridine to generate radicals in a mismatched region of DNA. We investigated a total of 12 variations of bases in the mismatched region. The oligonucleotides were irradiated with gamma-rays, and interstrand cross-link formation was analyzed by denaturing gel electrophoresis. We found that the efficiency of cross-link formation was highly dependent on the nature of mismatched bases and, on the basis of electrophoretic mobility, observed several distinctive cross-link structures with specific DNA sequences. This study provides new insights into the reactivity of mismatched DNA and the mechanisms leading to interstrand cross-link formation. The potential application of 5-bromo-2'-deoxyuridine-induced interstrand cross-links to the field of DNA repair is discussed.

Assessment of cell proliferation by 5-bromodeoxyuridine (BrdU) labeling for multicolor flow cytometry

Cell proliferation assays are used for a large variety of applications in the life sciences. This unit describes a flow-cytometry-based method that uses BrdU labeling in conjunction with multiple fluorescently labeled cell surface markers, allowing extensive phenotypic characterization of dividing cells in addition to assessment of their frequency. BrdU labeling has the advantage of constituting a nonradioactive technique that, when combined with additional fluorescent-based reagents, avoids time-consuming and often costly cell isolation procedures. Moreover, because BrdU is stably integrated into the DNA, it can be measured in a cell for many months. The method presented in this unit is based on paraformaldehyde fixation and reversible saponin-based cell membrane permeabilization, which maintains cell integrity as well as fluorescent labeling with a large number of different fluorochromes, allowing 10- to 12-color flow cytometric analysis of proliferating cells.

In vitro polydeoxyribonucleotide effects on human pre-adipocytes

OBJECTIVES

Adipose tissue is the most abundant and accessible source of adult stem cells. Human processed lipoaspirate contains pre-adipocytes that possess one of the a characteristic pathways of multipotent adult stem cells and are able to differentiate in vitro into mesenchymal and also neurogenic lineages. Because stem cells have great potential for use in tissue repair and regeneration, it would be significant to be able to obtain large amounts of these cells in vitro. As demonstrated previously, purine nucleosides and nucleotides mixtures can act as mitogens for several cell types. The aim of this study was to evaluate the effects of polydeoxyribonucleotides (PDRN), at appropriate concentrations, on human pre-adipocytes grown in a controlled medium, also using different passages, so as to investigate the relationship between the effect of this compound and cellular senescence, which is the phenomenon when normal diploid cells lose the ability to divide further.

MATERIALS AND METHODS

Human pre-adipocytes were obtained by liposuction. Cells from different culture passages (P6 and P16) were treated with PDRN at different experimental times. Cell number was evaluated for each sample by direct counting after trypan blue treatment. DNA assay and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide test were also carried out in all cases.

RESULTS AND CONCLUSIONS

PDRN seemed to promote proliferation of human pre-adipocytes at both passages, but cell population growth increased in pre-adipocyte at P16, after 9 days as compared to control. Our data suggest that PDRN could act as a pre-adipocyte growth stimulator.

Detection of S-phase cell cycle progression using 5-ethynyl-2'-deoxyuridine incorporation with click chemistry, an alternative to using 5-bromo-2'-deoxyuridine antibodies

The 5-bromo-2'-deoxyuridine (BrdU) labeling of cells followed by antibody staining has been the standard method for direct measurement of cells in the S-phase. Described is an improved method for the detection of S-phase cell cycle progression based upon the application of click chemistry, the copper(I)-catalyzed variant of the Huisgen [3+2] cycloaddition between a terminal alkyne and an azide. 5-ethynyl-2'-deoxyuridine (EdU) is a nucleoside analog of thymidine that is incorporated into DNA during active DNA synthesis, just like BrdU. While the BrdU assay requires harsh chemical or enzymatic disruption of helical DNA structure to allow for direct measurement of cells in the S-phase by the anti-BrdU antibody, the EdU method does not. Elimination of this requirement results in the preservation of helical DNA structure and other cell surface epitopes, decreased assay time, and increased reproducibility.

DNA replication during endospore development in Metabacterium polyspora

The guinea pig intestinal symbiont Metabacterium polyspora is an uncultured, endospore-forming member of the Firmicutes. Unlike most endospore-forming bacteria, sporulation is an obligate part of the M. polyspora life cycle when it is associated with a guinea pig. Binary fission is limited to a brief period in its life cycle, if exhibited at all. Instead, M. polyspora relies on the formation of multiple endospores for reproduction. Sporulation is initiated immediately after germination, which leaves little time for the cell to accumulate resources to support spore formation. Using immunolocalization of the nucleotide analogue bromodeoxyuridine (BrdU), we were able to follow replication dynamics in M. polyspora. BrdU was provided to cells within the guinea pig intestinal tract. BrdU was incorporated into DNA located within the forespores throughout development, at all stages prior to spore maturation. Our results suggest that in M. polyspora, DNA replication within the forespore is not suppressed during sporulation as it is in other endospore-forming bacteria. Replication within forespores would allow M. polyspora to maximize its reproductive potential and supply each endospore with at least one complete copy of the genome.

Evaluation of intestinal trophism: review of current methods and techniques

PURPOSE OF REVIEW

This review aims to cover the methods and techniques currently used by researchers to evaluate intestinal trophism.

RECENT FINDINGS

Although subjected to criticisms, conventional gut trophism evaluation by both morphological and histological parameters continues to be largely reported. The metaphase arrest technique and the detection of H-tymidine have been used less frequently in recent years due to increasing interest in the immunohistochemical methods such as 5-bromo-2'deoxy-uridine, Ki-67, and proliferating cell nuclear antigen. Along with common techniques for the evaluation of intestinal trophism, the combination of methods that includes a measurement of cell proliferation and an apoptotic index in the same study are most valuable and are increasing in the current literature.

SUMMARY

Evaluation of intestinal trophism is an important issue for both clinical and experimental nutritional studies. The immunohistochemical techniques are the gold standard to access cell proliferation. Evaluation of proliferation and apoptosis at the same time may offer a more reliable evaluation of the actual status of gut trophism.

Evaluation of intranuclear BrdU detection procedures for use in multicolor flow cytometry

BACKGROUND

Measurement of cell proliferation via BrdU incorporation in combination with multicolor cell surface staining would facilitate studies on cell subsets that require multiple markers for their identification. However, the extent to which the often harsh cell preparation procedures required affect the staining quality of more recently developed fluorescent dyes has not been assessed.

METHODS

Three cell preparation protocols for BrdU measurement were compared for their ability to maintain fluorescent surface staining and scatter parameters of in vivo BrdU-labeled cells by flow cytometry. A 10-color fluorescent panel was developed to test the quality of surface staining, following cell treatment and the ability to perform BrdU measurements on even small B lymphocyte subsets.

RESULTS

All cell preparation procedures affected the quality of fluorescent and/or scatter parameters to varying degrees. Paraformaldehyde/saponin-based procedures preserved sufficient fluorescent surface staining to determine BrdU incorporation rates among all splenic B cell subsets, including B-1a cells, which constitute roughly 0.5% of cells. Turnover rates of B-1a cells were similar to immature B cells and higher than those of the other mature B cell subsets.

CONCLUSION

Paraformaldehyde/saponin-based cell preparation procedures facilitate detailed cell turnover studies on small cell subsets in vivo, revealing new functional information on rare cell populations.